[2023-03-17 14:06:37,924] [INFO] DFAST_QC pipeline started.
[2023-03-17 14:06:37,924] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 14:06:37,924] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dfa6ec7-9efc-4e08-9a7c-c27e249ca6f4/dqc_reference
[2023-03-17 14:06:39,389] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 14:06:39,389] [INFO] Task started: Prodigal
[2023-03-17 14:06:39,389] [INFO] Running command: cat /var/lib/cwl/stgce9a3da1-40c6-44cd-bd40-517eb23d568c/OceanDNA-a14.fa | prodigal -d OceanDNA-a14/cds.fna -a OceanDNA-a14/protein.faa -g 11 -q > /dev/null
[2023-03-17 14:06:51,672] [INFO] Task succeeded: Prodigal
[2023-03-17 14:06:51,672] [INFO] Task started: HMMsearch
[2023-03-17 14:06:51,673] [INFO] Running command: hmmsearch --tblout OceanDNA-a14/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dfa6ec7-9efc-4e08-9a7c-c27e249ca6f4/dqc_reference/reference_markers.hmm OceanDNA-a14/protein.faa > /dev/null
[2023-03-17 14:06:51,808] [INFO] Task succeeded: HMMsearch
[2023-03-17 14:06:51,808] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgce9a3da1-40c6-44cd-bd40-517eb23d568c/OceanDNA-a14.fa]
[2023-03-17 14:06:51,823] [INFO] Query marker FASTA was written to OceanDNA-a14/markers.fasta
[2023-03-17 14:06:51,824] [INFO] Task started: Blastn
[2023-03-17 14:06:51,824] [INFO] Running command: blastn -query OceanDNA-a14/markers.fasta -db /var/lib/cwl/stg7dfa6ec7-9efc-4e08-9a7c-c27e249ca6f4/dqc_reference/reference_markers.fasta -out OceanDNA-a14/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:06:52,230] [INFO] Task succeeded: Blastn
[2023-03-17 14:06:52,230] [INFO] Selected 0 target genomes.
[2023-03-17 14:06:52,230] [INFO] Target genome list was writen to OceanDNA-a14/target_genomes.txt
[2023-03-17 14:06:52,230] [ERROR] File is empty. [OceanDNA-a14/target_genomes.txt]
[2023-03-17 14:06:52,230] [ERROR] Task failed. No target genome found.
[2023-03-17 14:06:52,231] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 14:06:52,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dfa6ec7-9efc-4e08-9a7c-c27e249ca6f4/dqc_reference/checkm_data
[2023-03-17 14:06:52,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 14:06:52,292] [INFO] Task started: CheckM
[2023-03-17 14:06:52,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a14/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a14/checkm_input OceanDNA-a14/checkm_result
[2023-03-17 14:07:27,835] [INFO] Task succeeded: CheckM
[2023-03-17 14:07:27,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.79%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 14:07:27,838] [INFO] ===== Completeness check finished =====
[2023-03-17 14:07:27,838] [INFO] ===== Start GTDB Search =====
[2023-03-17 14:07:27,838] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a14/markers.fasta)
[2023-03-17 14:07:27,838] [INFO] Task started: Blastn
[2023-03-17 14:07:27,838] [INFO] Running command: blastn -query OceanDNA-a14/markers.fasta -db /var/lib/cwl/stg7dfa6ec7-9efc-4e08-9a7c-c27e249ca6f4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a14/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 14:07:28,211] [INFO] Task succeeded: Blastn
[2023-03-17 14:07:28,212] [INFO] Selected 3 target genomes.
[2023-03-17 14:07:28,212] [INFO] Target genome list was writen to OceanDNA-a14/target_genomes_gtdb.txt
[2023-03-17 14:07:28,215] [INFO] Task started: fastANI
[2023-03-17 14:07:28,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgce9a3da1-40c6-44cd-bd40-517eb23d568c/OceanDNA-a14.fa --refList OceanDNA-a14/target_genomes_gtdb.txt --output OceanDNA-a14/fastani_result_gtdb.tsv --threads 1
[2023-03-17 14:07:29,231] [INFO] Task succeeded: fastANI
[2023-03-17 14:07:29,234] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 14:07:29,234] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_018652685.1	s__RBG-16-57-9 sp018652685	99.6052	369	382	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__TCS64;f__TCS64;g__RBG-16-57-9	95.0	99.72	99.64	0.95	0.93	7	conclusive
GCA_013619005.1	s__RBG-16-57-9 sp013619005	81.0657	192	382	d__Archaea;p__Thermoproteota;c__Bathyarchaeia;o__TCS64;f__TCS64;g__RBG-16-57-9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 14:07:29,234] [INFO] GTDB search result was written to OceanDNA-a14/result_gtdb.tsv
[2023-03-17 14:07:29,234] [INFO] ===== GTDB Search completed =====
[2023-03-17 14:07:29,235] [INFO] DFAST_QC result json was written to OceanDNA-a14/dqc_result.json
[2023-03-17 14:07:29,235] [INFO] DFAST_QC completed!
[2023-03-17 14:07:29,235] [INFO] Total running time: 0h0m51s